tbuckley/cabot-search huggingface dataset:
Abstract 3894: WNT5B in osteosarcoma stem cells
Authors: Rachel S. Perkins, Sarocha Suthon, Gustavo A. Miranda-Carboni, Susan A. Krum
Journal: Cancer Research (2022)

Abstract Osteosarcoma is a rare but deadly pediatric bone cancer. As it stands, there is no targeted therapy available for osteosarcoma. Therefore, patients are left with chemotherapy and surgical resection as their only treatment options. Further, osteosarcoma frequently metastasizes to the lungs and patients with metastatic disease have a dismal overall survival rate of 20% due to the lack of targeted therapy. Therefore, the goal of this study is to understand the role of the WNT5B signaling pathway in osteosarcoma, as it could be a potential therapeutic target. Using RNA sequencing from publicly available data sets and immunohistochemistry on tumor microarrays, we show that WNT5B is overexpressed in a subset of osteosarcoma patients. In these high expressing patients, WNT5B’s overexpression correlates to metastasis and worse overall survival. Due to the significant increase in WNT5B expression between primary tumors and metastasis, we began looking at the stem cell population of osteosarcoma cells. By selecting for the osteosarcoma stem cells using spheroid assays, we show that both protein and mRNA levels of WNT5B are enhanced in the stem cell population compared to the standard adherent cell population. Then, we looked at stemness markers and we show that WNT5B regulates the stemness gene SOX2. We then performed limiting dilution sphere assays to assess the role of WNT5B in sphere forming. We reveal that WNT5B is directly responsible for the sphere forming efficiency, as evidenced by a 50% reduction in spheres formed between 143B control and 143B WNT5B knockdown cells. Additionally, WNT5B drives proliferation and migration of osteosarcoma cancer stem cells as there is significantly decreased sphere size and migratory distance in WNT5B knockdown cells compared to control cells, and there is significantly increased sphere size and migration with the addition of recombinant WNT5B. Through revealing a novel role for WNT5B in osteosarcoma cancer stem cells, we present the WNT5B pathway as a candidate for therapeutically targeting the clinical implications of cancer stem cells, that is, the development of chemoresistance, metastasis and relapse. Citation Format: Rachel S. Perkins, Sarocha Suthon, Gustavo A. Miranda-Carboni, Susan A. Krum. WNT5B in osteosarcoma stem cells [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3894.
Dose-Dense Methotrexate, Vinblastine, Doxorubicin, and Cisplatin as the Gold Standard Neoadjuvant Chemotherapy Regimen for Patients With Nonmetastatic Muscle-Invasive Bladder Cancer Remains Controversial
Authors: Shuxiong Zeng, Zhensheng Zhang, Chuanliang Xu
Journal: Journal of Clinical Oncology (2022)

The result of an unblinded, multicenter, randomized phase III clinical trial (VESPER) was recently published by Pfister et al. 1 This study aimed to explore the optimal perioperative chemotherapy regimen for patients with nonmetastatic muscle-invasive bladder cancer (MIBC).The results of the study revealed that the dose-dense methotrexate, vinblastine, doxorubicin, and cisplatin (dd-MVAC) arm was related to a significant improvement of 3-year progression-free survival (PFS) compared with the gemcitabine and cisplatin (GC) arm in the setting of neoadjuvant chemotherapy (NAC) and suggested that dd-MVAC regimen should become the gold standard for NAC.Although the results of this study provide novel evidence for choosing optimal NAC regimen in patients with MIBC, a few pertinent issues of the study must be given due consideration before the results can be translated into daily clinical practice.
Abstract 5756: Next-generation sequencing (NGS) reveals different molecular profiles of pediatric sarcoma in children and adults
Authors: Weisong Cai, Fang Liu, Xuejiao Liu, Xiaojuan Wang, Chunyang Wang, Tonghui Ma, Shu Li
Journal: Cancer Research (2022)

Abstract Background: Pediatric sarcomas represent approximately 12% of all pediatric cancers with over 100 subtypes. Although some molecular detection techniques can be used to assist the diagnosis and treatment of pediatric sarcoma, it still remains challenging due to overlapping morphological features and limited biopsy specimens. Here we performed next generation sequencing (NGS) to analyze the molecular profiles of pediatric and adult sarcomas in China. Methods: A total of 700 Chinese patients with sarcoma were collected. The tumor tissue and matching blood specimens were tested by the integrative DNA and RNA sequencing panel Onco Panscan plus࣪ at Genetronhealth. Results: Of the 700 sarcoma patients, there were 224 children (32%) and 476 adults (68%). Difference from the almost same ratio of men to women in adults, there were more males (n = 134) than females (n = 90) in children. Rhabdomyosarcoma was the most common soft tissue tumor in children, accounting for 24.1% (n = 54), followed by Ewing's sarcoma (9.8%, n = 22) and Osteosarcoma (8.5%, n = 34), while Angiosarcoma (3.8%, n = 18) and Fibrosarcoma (3.6%, n = 17) were the most common in adults. Based on mutation types, the frequent alterations were missense mutations (n = 326, 51.2%), fusions (n = 129, 20.3%) and copy number variants (n = 66, 10.4%) in children with a mean of 3 mutations per patient, and missense mutations (n = 1438, 66.8%), fusions (n = 221, 10.3%) and truncating mutations (n = 215, 10.0%) in adults with an average 5 mutations. TP53 (12.9%, n = 29), EWSR1 (8.9%, n = 20) and ALK mutations (6.7%, n = 15) were common in children, which was distinct from TP53 (29.4%, n = 140), NF1 (4.8%, n = 23), CTNNB1 (4.2%, n = 20) and RB1 (4.2%, n = 20) in adults. Based on NGS results, pathological subtypes could be confirmed in 40.2% (90/224) and 48.1% (229/476) of children and of adults sarcoma patients, respectively. In addition, we identified a total of 72 drug-targeted gene mutations in the 57 children patients, of which 35 (48.6%) gene mutations could be targeted by FDA-approved drugs. In adults, 256 drug-targeted gene mutations were detected and the proportion of actionable mutations was up to 78.9% (n = 202). Conclusion: The genomic landscape of pediatric sarcomas is different from that of adults. NGS aids in the subtype classification and clinical guidance of pediatric sarcomas, providing evidence for personalized treatments with clinical benefit. Citation Format: Weisong Cai, Fang Liu, Xuejiao Liu, Xiaojuan Wang, Chunyang Wang, Tonghui Ma, Shu Li. Next-generation sequencing (NGS) reveals different molecular profiles of pediatric sarcoma in children and adults [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5756.
Abstract 1388: Mutations in transcriptional activators of MHC I antigen presentation, NLRC5 and CIITA, are mutually exclusive and have different effects on melanoma gene transcripts
Authors: Mildred Galvez, Katie M. Campbell, Egmidio Medina, Antoni Ribas
Journal: Cancer Research (2022)

Abstract Response to many immunotherapies depends on effective recognition and eradication of tumor cells by the immune system. This is mediated by the successful presentation of tumor-specific antigens on major histocompatibility complex class I (MHC I) molecules on the surface of tumor cells. Studies have focused on alterations in MHC I complex proteins (e.g. HLA, B2M) and gene regulatory elements (e.g. NLRC5). However, the impact on tumor response of individual defects in components regulating and composing the MHC I antigen processing and presentation machinery (APM) have not been extensively studied. Using a harmonized dataset of six clinical trials of patients with melanoma treated with ICB, whole-exome sequencing (WES, n= 244) and RNA sequencing (RNAseq, n= 426) data from untreated tumor samples were assessed to identify mutations in genes associated with MHC I APM and their regulation. Somatic alterations were correlated with clinical response to ICB and with gene expression profiles in tumor-matched RNAseq data. Mutations in MHC I and MHC I-related genes were found in 63% of patients (n= 154/244). The most recurrently mutated genes were NCAM1 (11%, n=28), TRIM48 (7%, n=17), and CAMK2B (6.6%, n=16), and the transcriptional regulators NLRC5 (9.4%, n=23) and CIITA (9.4%, n=23). Mutations in NLRC5 and CIITA trended toward being mutually exclusive from one another (Fisher’s exact test, p= 0.157) and mutations were overrepresented in tumors with stable or progressive disease following ICB therapy. In addition, lower expression of NLRC5 and CIITA were associated with stable or progressive disease status. NLRC5-mutant tumors that progressed following ICB therapy trended towards lower expression of transcriptional target HLA-A (Kruskal-Wallis, p=0.27); however, there was no difference in HLA-A expression across NLRC5-wildtype tumors. For class II transactivating factor, CIITA, which can induce MHC I expression, mutational status was not associated with HLA-A expression across all clinical response groups. There are genetic alterations spanning MHC I and MHCI-associated genes that may be responsible for inactivating class I antigen presentation by melanoma cells. The impact of these alterations may result in varied clinical responses to ICB therapies. The landscape of these alterations needs to be further delineated to understand how tumors are directly evading class I-mediated recognition and elimination. Citation Format: Mildred Galvez, Katie M. Campbell, Egmidio Medina, Antoni Ribas. Mutations in transcriptional activators of MHC I antigen presentation, NLRC5 and CIITA, are mutually exclusive and have different effects on melanoma gene transcripts [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1388.
Abstract 673: The EMT activator ZEB1 initiates polarized secretion of pro-tumorigenic effector proteins to drive lung adenocarcinoma progression
Authors: Guan-Yu Xiao, Xiaochao Tan, Leticia Rodriguez, Xin Liu, Jiang Yu, Mayra Vasquez, Hai Tran, William Russell, Don Gibbons, Jonathan Kurie
Journal: Cancer Research (2022)

Abstract There are few effective therapeutic options for metastatic lung adenocarcinomas (LUADs) that lack actionable mutations in receptor tyrosine kinases, and there is an urgent need to develop a better understanding of the biological basis of LUAD growth and metastasis. Our group has developed mouse models of LUAD metastasis and found that LUAD metastasis is epithelial-to-mesenchymal transition (EMT)-dependent. EMT causes cancer cells to switch their axis of polarity from apical-basal to front-rear, which orients organelles and actinbased cytoskeletal structures in ways that facilitate purposeful cancer cell motility and metastasis. The EMT-activating transcription factor ZEB1 silences microRNAs that target key inhibitors of the polarity axis switch. These data support the general belief that EMT-dependent metastasis is a cell-autonomous process. However, our new findings here show that ZEB1 coordinates the components of secretory trafficking machinery, Rab6A and Rab8A, via silencing miR-148a that target these effectors, to drive polarized secretory trafficking toward the leading edge of LUAD cells, to enhance surface exposure of MMP14 so that triggers ECM degradation, accelerates focal adhesion turnover and promotes cancer cell migration. Moreover, the ZEB1-driven secretory trafficking increases the secretions of cytokines and immunomodulation factors, to generate an immunosuppressive tumor microenvironment, and to promote LUAD metastasis. These findings advance a paradigm in which EMT drives LUAD metastasis through a cell non-autonomous mechanism. The novelty rests in our results that demonstrate a transcriptional governance of polarized vesicular transport, providing the potential to target ZEB1-driven secretory pathways for the purpose of blocking metastasis in LUAD. Citation Format: Guan-Yu Xiao, Xiaochao Tan, Leticia Rodriguez, Xin Liu, Jiang Yu, Mayra Vasquez, Hai Tran, William Russell, Don Gibbons, Jonathan Kurie. The EMT activator ZEB1 initiates polarized secretion of pro-tumorigenic effector proteins to drive lung adenocarcinoma progression [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 673.
Abstract 2830: Multiplexed shRNAs targeting FAS and PTPN2 enhance CAR T persistence and anti-tumor efficacy
Authors: John Gagnon, Adam J. Litterman, Jason A. Hall, Dina Polyak, Stanley Zhou, Sahil Joshi, Oliver Takacsi-Nagy, Hans Pope, luisa silva, brenal K. Singh, jeffrey M. Granja, david DeTomaso, Edgar Aristil-Lepe, Michelle Tan, Brendan Galvin, Grace X. Zheng, Stephen Santoro, Aaron Cooper, Natalie Bezman, W Nicholas Haining
Journal: Cancer Research (2022)

Abstract Cell therapies have shown limited efficacy in solid tumors, in part due to limitations in CAR T cell survival, expansion, and resistance to immunosuppressive pathways operating in the tumor microenvironment (TME). To overcome these hurdles, we screened a library of 171 pair-wise gene knockouts using CRISPR-Cas9 to identify gene pairs that confer greater proliferation and persistence with repetitive stimulation. Combined KO of FAS and PTPN2 led to a significant improvement in T cell effector function and proliferative capacity. FAS, the receptor for FASLG, is highly expressed on patient-derived T cells and has been shown to induce T cell apoptosis and limit T cell persistence in the TME. PTPN2 is a phosphatase, in which deletion increases T cell proliferation and cytotoxicity. To develop this clinically, we generated CAR T cells with a shRNA module capable of multiplexed knockdown of both FAS and PTPN2. The FAS/PTPN2 shRNA module protected T cells from FAS-mediated apoptosis and resulted in a marked increase in T cell expansion over the course of a repetitive stimulation assay. Consistent with these observations, RNAseq analysis revealed enhanced transcriptome-wide signatures of cell cycle and T cell effector function. Finally, in a tumor xenograft model, CAR T cells containing FAS/PTPN2 shRNA module demonstrated significantly improved tumor control in addition to increased cell numbers in circulation compared with CAR T cells expressing an irrelevant shRNA module. The use of a multiplexed shRNA module is a powerful approach to improve T cell intrinsic functionality in cellular therapies, enabling: 1) tailored levels of inhibition of multiple key regulators of T cell biology with constitutive or antigen-gated expression, and 2) a method for genetic perturbations in T cells with reduced risk of toxicity or transformation compared with multiple DNA edits. The FAS/PTPN2 shRNA module described here will be tested as a component of AB-1015, an integrated circuit T cell therapy for solid tumors expressing ALPG and mesothelin. Citation Format: John Gagnon, Adam J. Litterman, Jason A. Hall, Dina Polyak, Stanley Zhou, Sahil Joshi, Oliver Takacsi-Nagy, Hans Pope, luisa silva, brenal K. Singh, jeffrey M. Granja, david DeTomaso, Edgar Aristil-Lepe, Michelle Tan, Brendan Galvin, Grace X. Zheng, Stephen Santoro, Aaron Cooper, Natalie Bezman, W Nicholas Haining. Multiplexed shRNAs targeting FAS and PTPN2 enhance CAR T persistence and anti-tumor efficacy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2830.
Abstract 1357: T cell memory and the critical effectors of successful anticancer immune response
Authors: Andrew Daniels, William Damsky, Meaghan McGeary, Akiko Iwasaki, Marcus Bosenberg
Journal: Cancer Research (2022)

Abstract Despite the initial clinical success of immunotherapies in the treatment of melanoma, most patients fail to achieve long-term responses. While the majority of patients initially respond to these treatments, most go on to develop secondary resistance. The mechanisms underlying this failure of long-term response and successful responses is poorly understood. To better understand the factors contributing to successful long-term anti-cancer immune responses, we utilized the YUMMER1.7 (YR1.7) melanoma line to develop a novel model for the evaluation of immunologic memory. We found that mice engrafted with a YR1.7 tumor can be cured by resection, and that subsequent challenge of these mice with the same tumor, even at 20x the cell number, led to expeditious rejection. Using depleting antibodies, we found that memory response were dependent on CD8 and CD4 T cells, and that CD4 depletion alone does not compromise initial responses, but leads to eventual failure of memory. We found no effect of natural killer cell (NK) depletion. We performed single cell RNA sequencing on primary and rechallenge tumors from the same mouse, with the same tumor line. We found a phenotype of clonal replacement, in which the effective T cell clones seen in the memory response were non-overlapping with those found in the primary tumor. This implies an extra-tumoral location for these clones in the primary setting or the potential for additional priming of novel T cell clones upon re-challenge. Together, these findings suggest a novel insights on the manner and location of T cells needed for anti-cancer memory responses. Citation Format: Andrew Daniels, William Damsky, Meaghan McGeary, Akiko Iwasaki, Marcus Bosenberg. T cell memory and the critical effectors of successful anticancer immune response [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1357.
Abstract 576: Shark VNAR single domain-based CAR T cells targeting PD-L1 for cancer therapy
Authors: Dan Li, Hejiao English, Jessica Hong, Tianyuzhou Liang, Glenn Merlino, Chi-Ping Day, Mitchell Ho
Journal: Cancer Research (2022)

Abstract Background: Chimeric antigen receptor (CAR)-T therapy shows great potency against hematological malignancies, whereas it is difficult to transfer CAR T into solid tumors due to lack of appropriate antigenic targets and immunosuppressive tumor microenvironment. Checkpoint molecule PD-L1 is widely overexpressed on multiple tumor types, and PD-1/PD-L1 interaction is a primary mediator of immunosuppression in the TME. Here, we generated anti-PD-L1-specific shark single domain VNAR-based CAR T cell strategy and explored its anti-tumor efficacy in xenograft mouse models. Methods: We isolated anti-PD-L1 single domain antibodies from semi-synthetic shark VNAR phage display libraries. The binding of isolated VNARs was validated by ELISA, flow cytometry, and Octet. A peptide library based on human PD-L1 was synthesized to predict the epitope of select VNARs. Anti-tumor efficacy of CAR T cells was determined via cell luciferase-based cell assay as well as xenograft mouse models. Two tumor models, MDA-MB-231 (triple-negative breast cancer) and Hep3B (hepatocellular carcinoma or HCC) were used in the present study. Glypican-3 (GPC3) is a tumor-specific target in the Hep3B model. Results: We identified three anti-PD-L1 phage binders, B2, A11, and F5 from our shark phage libraries. All three binders showed cross-activity to human, mouse, and canine antigens, whereas only B2 functionally blocked the interaction of human PD-1 to PD-L1. Moreover, CAR (B2) T cells specifically lysed both MDA-MB-231 and Hep3B tumor cells by targeting constitutive and inducible expression of PD-L1. Importantly, the combination of anti-GPC3 CAR (hYP7) T cells with CAR (B2) T cells regress Hep3B tumors synergistically in mice. Conclusions: PD-L1-targeted shark VNAR single domain-based CAR T cell therapy is a novel strategy to treat breast cancer and liver cancer. This work provides a rationale for a potential use of anti-PD-L1 CAR T cells as a monotherapy or combination with a tumor-specific therapy in clinical studies for solid tumors. Citation Format: Dan Li, Hejiao English, Jessica Hong, Tianyuzhou Liang, Glenn Merlino, Chi-Ping Day, Mitchell Ho. Shark VNAR single domain-based CAR T cells targeting PD-L1 for cancer therapy [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 576.
Abstract 956: Role of E-cadherin in progression of invasive breast lobular carcinoma
Authors: Laura Savariau, Nilgun Tasdemir, Ashuvinee Elangovan, Kai Ding, Pooja Sree Tallapaneni, Jagmohan Hooda, Jennifer M. Atkinson, Adrian V. Lee, Steffi Oesterreich
Journal: Cancer Research (2022)

Abstract Invasive lobular carcinoma (ILC) is the second most frequently diagnosed histologic subtype of invasive breast cancer following invasive ductal carcinoma (IDC) and accounts for 15% of all cases. The hallmark of ILC is the genetic loss of E-cadherin (CDH1) causing the disruption of adherens junctions and resulting in discohesive, linear growth of ILC cells in tissues. Beyond its effects on this unique histology, there is limited data on the role of E-cadherin loss in ILC metastasis. Therefore, we generated three ILC cell lines (MDA-MB-134, SUM44PE and BCK4) with inducible E-cadherin overexpression. Using immunoblotting and immunofluorescence microscopy we confirmed E-cadherin expression, re-expression of other adherens junction proteins including α and β-catenin, and re-localization of cytoplasmic p120-catenin to the membrane. Successful cell adhesion to E-cadherin coated plates suggested formation of functional junctions. E-cadherin expression had no effect on 2D growth but did diminish cell growth in ultra-low attachment (ULA) conditions consistent with its previously described role in anoikis. We confirmed increased cell death of MM134 with E-cadherin overexpression compared to control cells when grown in ULA. Overexpression of E-cadherin failed to rescue poor migratory and invasive ability of ILC cell lines as measured by transwell assays. However, E-cadherin expression in SUM44PE lead to decreased haptotaxis to collagen I, and altered morphology from loose grape-like structure to tight sphere-like formation when embedded in collagen I.In vivo analyses revealed reduced primary tumor formation in E-cadherin-overexpression SUM44PE cells after mammary fat pad injection. Additional studies aimed at understanding E-cadherin’s effect on in vivo metastasis are ongoing.Collectively, our studies using novel cell line models will lead to an improved understanding of the hallmark loss of E-cadherin and disease mechanisms in ILC, which we hope will ultimately enable the development of more effective therapies and improve the outcome of patients with this understudied histological subtype of breast cancer. Citation Format: Laura Savariau, Nilgun Tasdemir, Ashuvinee Elangovan, Kai Ding, Pooja Sree Tallapaneni, Jagmohan Hooda, Jennifer M. Atkinson, Adrian V. Lee, Steffi Oesterreich. Role of E-cadherin in progression of invasive breast lobular carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 956.